A 1,3-dipolar cycloaddition, also called Huisgen (3+2) cycloaddition, is a chemical reaction between a 1,3-dipole and a dipolarophile to form a five-membered ring. Typical dipoles that are used in (3+2) cycloaddition reactions involve azides, nitrones, nitrile oxides and diazo compounds, to react with alkynes or alkenes as dipolarophile, leading to five-membered heterocycles. Typical conditions for Huisgen cycloaddition involve the prolonged heating of starting components. However, cycloaddition can also be induced by means of addition of a metal catalyst or by means of the use of a strained alkene or alkyne.
Strain-promoted azide-alkyne cycloaddition (SPAAC) involves the formation of a 1,2,3-triazole by reaction of an azide with a strained, cyclic alkyne. Apart from azides, strained alkynes also show high reactivity with other dipoles, such as nitrones and nitrile oxides. For example, the strain-promoted alkyne-nitrone cycloaddition (SPANC) was applied for the N-terminal modification of proteins.
SPAAC and SPANC cycloaddition reactions proceed spontaneously, hence in the absence of a (metal) catalyst, and these and a select number of additional cycloadditions are also referred to as “metal-free click reactions”.
Original reports on the reaction of phenyl azide with cyclooctyne date back more than 50 years, but it was not until 2004 that the practical use of SPAAC was recognized for the functional connection of two molecular entities, connected to azide or cyclooctyne, respectively. For example, Bertozzi et al. have demonstrated in J. Am. Chem. Soc. 2004, 126, 15046 (incorporated by reference) that incubation of Jurkat cells with azide-functionalized mannosamine led to effective exposure of azide on the cell surface, as visualized by treatment with cyclooctyne-conjugated biotin, then staining with FITC-avidin and flow cytometry. However, it was also found that the reaction rate of plain cyclooctyne with azide was relatively low, for example less effective than similar staining of azide-labeled cells with copper-catalyzed cycloaddition of azide with a biotinylated terminal alkyne (CuAAC) or with a phosphine reagent (Staudinger ligation). As a consequence, in subsequent years much attention has been focused on the development of cyclooctynes with superior reaction rates, for example difluorocyclooctyne (DIFO), dibenzocyclooctynol (DIBO), dibenzoazacyclooctyne (DIBAC/DBCO), bisarylazacyclooctynone (BARAC), bicyclo[6.1.0]nonyne (BCN) and carboxymethylmonobenzocyclooctyne (COMBO). Of these, the most frequently applied cyclooctynes are DIBO, DIBAC/DBCO and BCN, all of which are commercially available and display high reactivity in cycloadditions not only with azides, but also with other 1,3-dipoles such as nitrones, nitrile oxides and diazo compounds.

An example of a cyclononyne is the benzocyclononyne shown below, disclosed by Tummatorn et al., J. Org. Chem. 2012, 77, 2093, incorporated by reference.

The ease of operation of SPAAC and the high stability of the resulting triazole functionality have led to a wide range of applications, including in vitro and in vivo labeling, patterning of solid surfaces, formation of bioconjugates from proteins, nucleic acid and glycans, medical applications etc. Two prime parameters that determine the choice of cyclooctyne for a particular application are lipophilicity and reaction rate. Since the vast majority of cyclooctynes exist predominantly of hydrocarbon, they are typically hydrophobic and hence poorly water-soluble. To enhance water-solubility, Bertozzi et al. developed dimethoxy-azacyclooctyne (DIMAC) from a carbohydrate precursor, as reported in Org. Lett. 2008, 10, 3097 (incorporated by reference), but the increase in polarity was accompanied by attenuated reactivity. Two successful strategies to enhance water-solubility of a benzoannulated cyclooctyne, as was demonstrated for derivatization of DIBO, are by aromatic sulfonation (Boons et al., 2012, 134, 5381, incorporated by reference) or by tetramethoxy-substitution (Leeper et al. 2011, 2, 932, incorporated by reference). However, it is also clear that from a steric perspective it is more desirable to avoid the presence of a (bulky) substituent in a cyclooctyne altogether. Thus, the desire to optimize hand-in-hand polarity and reactivity of cyclooctynes is still driving research for further improvement.
In a recent report, Bertozzi et al. in J. Am. Chem. Soc. 2012, 134, 9199, incorporated by reference, explicitly mention that BARAC reacts with azide faster than any other reported cyclooctyne, thereby underlining the general perception that reaction rate of cyclooctynes is not influenced by azide substituents (aliphatic or aromatic or substituted versions).
A halogenated aryl azide with particular application in the field of labeling is 4-azido-2,3,5,6-tetrafluorobenzoic acid (N3-TFBA). Originally introduced by Fleet et al. in Nature 1969, 224, 511, incorporated by reference, aryl azides have become popular precursors of nitrenes as versatile photoaffinity labeling agents. Upon photolysis, N2 is liberated and a highly unstable singlet phenylnitrene is formed in situ, which reacts with neighbouring molecules in a variety of reactions. Perfluorophenyl azides are of particular interest in the field of photoaffinity labeling because highly stabilized nitrene intermediates are formed that undergo insertion and addition reaction in moderate to good yields rather than intermolecular rearrangements. For this purpose, a variety of derivatives of 4-azido-2,3,5,6-tetrafluorobenzoic acid (N3-TFBA) are commercially available and have been applied for labeling of biomolecules, polymers, small molecules, carbon materials, gold/silver, metal oxides and silicate/semiconductors, as inter alia reviewed in Liu et al. Acc. Chem. Res. 2011, 43, 1434 and Welle et al. Synthesis 2012, 44, 2249, both incorporated by reference. However, none of the earlier applications of N3-TFBA mention labeling or conjugation by strain-promoted cycloaddition reaction.